phosphonormalizer
This is the development version of phosphonormalizer; for the stable release version, see phosphonormalizer.
Compensates for the bias introduced by median normalization in
Bioconductor version: Development (3.24)
It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.
Author: Sohrab Saraei [aut, cre], Tomi Suomi [ctb], Otto Kauko [ctb], Laura Elo [ths]
Maintainer: Sohrab Saraei <sohrab.saraei at blueprintgenetics.com>
citation("phosphonormalizer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("phosphonormalizer")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("phosphonormalizer")| Pairwise normalization of phosphoproteomics data | HTML | R Script |
| phosphonormalizer: Phosphoproteomics Normalization | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Normalization, Proteomics, Software, StatisticalMethod, WorkflowStep |
| Version | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.0) |
| Imports | plyr, stats, graphics, matrixStats, methods |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | MSnbase |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | phosphonormalizer_1.37.0.tar.gz |
| Windows Binary (x86_64) | phosphonormalizer_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | phosphonormalizer_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | phosphonormalizer_1.37.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/phosphonormalizer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/phosphonormalizer |
| Bioc Package Browser | https://code.bioconductor.org/browse/phosphonormalizer/ |
| Package Short Url | https://bioconductor.org/packages/phosphonormalizer/ |
| Package Downloads Report | Download Stats |